![]() ![]() ![]() Now all bonds have been given the type "A-A" based on being between bonds of two atoms with type "A". In this specific system, all atom types are the same, so there should be only one bond type: TopoTools contains a script that helps with assigning bond types according to this convention. In many classical MD packages, the bond type is derived from the atom types that form the bond. This step does not assign any bond type (or bond order) information, but rather define it as "unknown". Thus 0.6 * (0.85+0.85) = 1.02 which is larger than 1.0, so there will be a bond between each atom and its direct neighbor(s): In the example coordinate file, that atoms are 1.0 units apart and we have set the radius to 0.85. The algorithm implemented by VMD is simple: if the distance between two atoms is shorter than 0.6 times the sum of their radii, those atoms are considered to have a bond. This now is sufficient to compute the bonds from atom distances. This specific system is to be used with reduced units (units lj in LAMMPS input) and thus we need to set a reasonable radius and mass value. This is done by creating an atom selection and then assigning properties to all atoms in that selection: ![]() Now we need to assign data to the atoms that is required for writing a proper LAMMPS data file, but not available in the. We use the autobonds no flag to inhibit any automatic bond searches: mol new chain.xyz autobonds no waitfor all The next step is to load the molecular coordinate data. This test makes it look a bit more complicated, but effectively this is the same as these two lines: package require topotools The first block of script code loads the TopoTools and pbctools plugins and makes sure that they are of a sufficiently high version. This paragraph discusses the simplexyztodata.tcl script. ![]()
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